I have most of my lights with Z-wave dimmers and switchers and they work ok, no issue there. However I noticed that when I trigger these manually (from the wall pad that sends the wired signal to the for example Fibaro switch), Domoticz does not have a log of it. I can see the logs when Domoticz triggers the event, but not when manually overrided by the wall switch.

Is this normal behaviour? I was keen to know more about my routines to start digging into ML....

Could you check in the manual if there is a 'group' that notifies the controller that there are updates ?
For example this could be Group 3, in that case, from the OpenZWave setup, select Groups&Network from the dropdown,
and add Node 1 (the controller) to this group for that node

I am sorry but can't read that screen shot properly. It does look like there is a number in Group 1, which is the group the controller needs to be in.
Is that the controller number there?

EDIT: So it is the other way round: in this case the device group 1 needs to have deviceid of the controller in it. This should be the case for all devices, although the group ID can differ per device.

You are a little confused here.
So lets take de Hall. It has in Group1 the device 1 ( did you replace your controller that had deviceid 1 at the time?)
This group1 needs to contain the deviceid of your current controller, so should be 61.
There is no need to add anything to the controller itself, only to each device you want to control and receive the status for!
So when this work for Hall, you need to check/update all ZWAVE devices.
By the way: the CO2 sensor and Kitchen do have the proper value there (61) so guess they work fine?